I agree, but when he's less super soldiery, then it undermines his leadership, where he has to prove it to random cops. It also makes him less appealing overall, so that Stark ends up being the actual leader, and Cap is just the field commander. "Call it Cap."

I don't think it undermines his leadership. He just looks weaker than he actually is, and that lies specifically with his super soldier abilities, not his leadership. He only had to prove himself to those cops because they didn't know who he was, but once he took the aliens down he got their respect.

Stark was never seen as the leader in the movie. Him saying "Call it, Cap" just showed that he trusted Cap to call the shots, as did the rest of the team when no one gave any objections. I understand what you're saying about Cap's physical prowess, but he was clearly seen as the leader of the team and a leader of men.